Syntax - Science topic

Need details on this please!

GROMACS version: 2022.4 Hi, I am working with a GPCR system embedded in lipid bilayer and water. I want to select every water (group 31 in index file) that is situated below 4A from a particular residue of the protein (group 43), so the command has been used as I have seen being used in earlier queries: gmx select -f input.xtc -s input.tpr -n input.ndx -select ‘group 31 and within 0.4 of group 43’ -on output.ndx

But I get multiple syntax errors: Error in user input: Invalid command-line options In command-line option -select Invalid selection ‘and’ Near ‘and’ syntax error In command-line option -select Invalid selection ‘within’ While parsing ‘within’ ‘within’ should be followed by a value/expression ‘of’ is missing In command-line option -select Invalid selection ‘0.4’ Near ‘0.4’ syntax error In command-line option -select Invalid selection ‘group’ Near ‘group’ syntax error In command-line option -select Near ‘�’ syntax error Where am I going wrong? I have tried few other combinations too, but those were also followed up similar syntax errors? Thanks in advance

Dear researchers, I am trying to assess specific indirect effects in my model with three moderators. However, AMOS always gives a syntax error and my estimand could not run. When I try it on R studio (with lavaan and psych packages), I could not assign parameters to calculate specific indirect effects. Could you please help me identify problems and solutions for this?

Below is the code in R studio:

library(psych)

library(lavaan)

# I already input my CSV data so now I just describe it

describe(my.data)

A =~ A2+ A3 + A4 + A5 + A7 + A8

MS =~ MS1 + MS2 + MS3 + MS4 + MS6 + MS7+ MS8

M =~ M1 + M2 + M4 + MA8

IM =~ IM1 + IM2 + IM3 + IM4

FLA =~ Listen + Speak + Read + Write

# Regression paths from IV to mediators

M ~ a1*IM

A ~ a2*IM

MS ~ a3*IM

# Regression paths from mediators to DV (FLA)

FLA ~ b1*M + b2*A + b3*MS + c1*IM

#From this moment, I tried to assign parameters to calculate specific indirect effects. However, none of the below functions works!

direct : c1

Error: object 'direct' not found

direct:= c1

Error in `:=`(direct, c1) : could not find function ":="

direct<-c1

Error: object 'c1' not found

direct=c1

Error: object 'c1' not found

“Machine learning tells us nothing!!!!  It [human language] is too rich. … It [language] works as well with impossible languages as with regular languages. … [AI] is as useful as a bulldozer is useful. …  It tells you nothing about mind and thoughts. …  Computational complexity is what accounts for language. …  [AI] will never provide [an] explanation to language. …  Syntax gives language meaning…and syntax is totally independent of the external world [and is controlled by the brain].” (Chomsky, N., 2022, On Theories of Linguistics (Part 2), Dec. 30, 42.32 minutes, Youtube).

If Noam Chomsky is correct that his Universal Grammar, as controlled by the brain, is independent of the external world, then ChatGPT—which is based on vacuuming large amounts of information from the external world—will never be a suitable metaphor for human language.  Furthermore, AI was not designed to provide meaning to its output and that it is merely a transmitter of an output that underwent a previous reconfiguration (i.e., a Factor Analysis that can act on its input). Therefore, the creativity attributed to AI—with its high energy cost as compared to that of the biological brain—will, at best, remain a tool in the hands of humans.  This of course is good news, since humans need to be held responsible for all actions (good and bad) generated by AI (Harari 2024).

I want to adopt an embedded Research Design for my PhD thesis and proposal. Please guide me and help me develop an analysis plan for my Research Design along with the suggested target population and sampling techniques so that I can help significantly through artificial intelligence the teachers speed up the ASL and ESL language learners' learning to combat common teaching barriers such as unfriendly behavior and unengaging behavior of the teachers. The respondents can be comparatively taken online ( i.e., schools, colleges, universities, or others) through the AIs respondents and manually. How can be all five chapters of my thesis and proposal if my title is," From Syntax to Semantics: Exploring AI-Enhanced Teaching Tools for English and Arabic Language Learners" and also develop the research questions and questionnaire items both in English and Arabic.

I am carrying out a research on patients with sarcopenia related to fracture rate, using SF-12 version 2 as the QoL tool.

I was wondering if anyone is using the same questionnaire and calculate the scores using SPSS syntax? Thank you very much!

In one of my Phd papers, I have cross-sectional dependence problem among the panels. I thus need to test for presence of unit roots. From literature, I note that there are two panel unit root tests that take into account cross-sectional dependency: Pesaran (CIPS) test and Bai and Ng test. I know the code for the former in Stata, but am not aware of the code for the later. Kindly please assist.

Kind regards

Sopani (gsopani@gmail.com)

Hello everyone, I use IBM SPSS Statistics 29.0.2.0 and I have a list of the following dichotomous variables:

This is an example of how they are coded: {1.00, No household members who are self-employed} and {2.00, Household members who are self-employed}. Of course, each one has its corresponding values. Now, I want to compute all of these variables into one comprehensive dichotomous variable called: Household economic activity status with the following values: 1.00, Households with at least one Economically Active Member and 2.00, Households with at least one Economically Inactive member.

I tried running different codes on the syntax, but none worked. I would greatly appreciate any help on how to do this.

Thanks and best wishes,

Amina

Hi there,

I was looking for a scoring guide or SPSS/Stata/R syntax for scoring SF 12 version-2. Can anyone help me in this regard? My email address is m.alimam@cqu.edu.au

Thanks in advance.

I'm trying to use this novel material (LaZrO2) as a gate oxide in SOI using 'user.material' syntax but getting an error

1. a. Who_j knows who_k heard what stories about himself_k?

b. John does (=John knows who_k heard what stories about himself_k).

2. a. Who_j knows what stories about himself_j who_k heard?

b. John does (=John knows what stories about himself_j who_k heard

/John knows who_k heard what stories about his_j own)

The examples (1a) and (2a) ask questions about the matrix subject 'who', with 'John' italicized in (1b) and (2b) corresponding to the wh-constituents that are being answered. I am curious about the binding relations in these examples, particularly in (2). Can example (2a) be construed as a question target matrix subject 'who' with 'himself' bound by the matrix subject?

Recently I was suggested to do Parallel Analysis and compare with EV>1 to determine no of factors for my scale. However, the scale I have developed uses Principal Axis Factoring and not PCA. If I use the SPSS syntax for Common Factor Analysis as given by Connors, all the mean EVs are less than 1.If I am using PCA then I am getting some factors with mean values greater than 1. I am confused as how to proceed further as the constructs in my scale are correlated and not suitable for PCA theoretically. Do I still proceed with Parallel Analysis?

Usually we use .fchk files (Gaussian) for fcclasses to generate .fcc files for running fcclasses. But, we have optimised the geometries using ORCA which generated .out, .hess, .grad files. Though Fcclasses help is suggesting that .hess file can be used instead of .fchk, we're facing errors. Giving suggestions on syntax will help us a lot.

Hi everyone,

I have conducted multigroup sem in JASP. I got measurement invariance test results that I expected. Now, I wonder to know how I can write the syntax showing constrained path to be equal in two groups. I could not find any explanations about it. Thank you for your answer

Hi everyone,

I tested a traditional 2-1-1 MLM based on the Mplys syntax example of Preacher

(see https://www.statmodel.com/download/Preacher.pdf for more info).

I specified for standardized output in the syntax, which I received for the direct effects and path coefficients etc. The problem is that I did not get standardized estimates for the calculated indirect effects but only unstandardized coefficients. I was looking for the answer on why this is, but I can only seem to find papers who also report unstandardized estimates for indirect effects yet don't explain why.

So in short, why are standardized estimates for indirect effects of multilevel mediation models in Mplus not included in the output even though I requested it?

Cheers,

Maria

I have tries "a_nonSchmid_110" or "a_nS" in the material.yaml file, but none of these works. Help is highly appreciated.

Somebody who give me a syntax for SAS software to determine de letal concentration on probit analysis?

I am trying to conduct an a priori Monte Carlo power analysis for a multi-group path analysis. Does anyone have a sample syntax for Mplus or a reference? I have collected effect sizes for each of my paths but I am not sure how to calculate the parameter estimates

Is anyone using MFT to calculate J , then which code are you using...is it possible by DFT .. IF yes then what will be the syntax for it , can u explain by giving a simple example.

Hello, I'm quite new here.

I'm just following a tutorial based on the folding Trp Cage Amber tutorial.

When I try to do the minimization with the following code:

pmemd -O -i 1min.in -o 1min.out -p TC5b.prmtop -c TC5b.inpcrd -r 1min.ncrst -inf 1min.mdinfo

it returns me:

"Error: Error from the parser: syntax error.

Check for typos, misspellings, etc. Try help on the command name and desc on the command arguments"

It seems that there is a syntax error but I can't find out which is it.

Could someone help me? Thank you very much

Words get thrown around. Terminology changes. Therefore, syntax is center of linguistics.

i am trying to make a GUI interface for my modelings but a syntax error are emerged.

how can i solve this error?

GUI codes are attached...

transitivity Analysis can identify the development of the human language according to the analysis done by Halliday and Roqaia Hassen on the work of William Golding's novel " the inheritors"

Right now I am wondering what I might be possibly doing wrong with my SPSS syntax. I have got 2 already dichotomized variables and I would need to combine them to make the 3rd one.

If var1 and var2 = 0, than it should be 0, and if var1 or var2 = 1 (or both of them), then it should be 1.

I tried this syntax (and many more :D), it is just not working.

I want to run FMOLS and DOLS in stata. Can someone share the syntax or help me guide about the process?

what is the relationship between syntax and syntax ?

this is what they say on etymoline.com:

"late 14c., auctorisen, autorisen, "give formal approval or sanction to," also "confirm as authentic or true; regard (a book) as correct or trustworthy," from Old French autoriser, auctoriser "authorize, give authority to" (12c.) and directly from Medieval Latin auctorizare, from auctor (see author (n.))."

What are some (esoteric) programming languages whose syntax comes closest

to natural language ? An example usually given is Perl which was developed by a linguist.

Personally I find that functional programming is closer to natural language than procedural programming.

• Yiddish is the language of sarcasm and irony. It is also the language of Jewish culture. Richard Fein’s experiences were typical:

• “Yiddish was in my bones, but hidden from my tongue. I did not know Yiddish as a language, but I felt reared in its resonance, pitch, and tone. I recognized a few words uttered in isolation, grasped nothing of its structure, but felt washed in its rhythms. Although I could not speak Yiddish, it was not a foreign language. I never possessed it, but sensed it possessing me.”

CASE GRAMMAR: A MERGER OF SYNTAX AND SEMANTICS

Charles Fillmore’s Deep Cases are determined not by syntax, but rather by semantics. Rather than having Subject, Indirect Object and Direct Object, Fillmore uses such terms as Agent, Experiencer, Instrument, and Patient.

The semantic features often occur in contrasting pairs, like Animate vs. Inanimate, and Cause vs. Effect. Thus:

Agent: Animate Cause

Experiencer: Animate Effect

Instrument: Inanimate Cause

Patient: Inanimate Effect

In an Active Sentence the most active Deep Case is eligible to become the Subject and the least active is eligible to become the Direct Object.

In a Passive Sentence the least active Deep Case is eligible to become the Subject and the most active case becomes an Object of the Preposition “by.”

Normally, the most active deep case is selected as the subject of the sentence:

The Actor if there is one

If not, the Instrument if there is one

If there is no Actor or Instrument, the Object becomes eligible. Therefore we have the following:

The boy opened the door with the key.

The key opened the door.

The door opened.

Is Case Grammar an effective method for showing the interrelationships between syntax and semantics?

Hi,

I have just installed and used spss 29. I was using spss 27.

I am analyzing data with a crossed random effects mixed model.

I am using syntax for this type of analysis. With the exact same syntax and data base I obtain different results with spss 29 and spss 27!

Specifically, the same model (that I call model 3) run with spss 27 was not giving me a warning whereas with spss 29 I get a warning (The final Hessian matrix is not positive definite although all convergence criteria are satisfied. The MIXED procedure continues despite this warning. Validity of subsequent results cannot be ascertained.).

Another case: with a slightly simpler model that I call model 2, I have no warnings but the results with spss 27 and spss 29 are not identical (e.g. BIC is different).

Is anyone experiencing the same or similar ?

Hi all,

I previously ran Little's MCAR test in mplus (all variables are categorical), but I am unable to find the syntax/steps to run it now. Can anyone point me in the correct direction in where to find this syntax/code/steps?

Thank you all so much!

I am currently initiating Calphad optimization for my experimental phase diagram construction, and I want a complete list of the items (keyword, operator, etc.) of .pop file.

Although I managed to get explanative documentation from Thermocalc and Computherm (Pandat), it is more like a case study rather than a complete explanation.

We are recoding our data and transforming the data values into the values we won't according to the questionaries we have used and its scores.

The first couples of recodes went fine, and we can see the values in the Data view after we ran the syntax. But then all of a sudden after we ran a recode of the next variable in our syntax, the value did not show in the Data view, and instead of the value, the columns just have a dot; .

We don't have any missing values, and the original data, we are recoding, has values. So what are we doing wrong, can any body help us?

We have been checking the syntax over and over again, to see if we are doing something diffrent form the first couples of recodes, where nothing is wrong.. but we can't find any differences.

Dear all,

I installed the latest Vina version on my conputer and as everyone knows, it does not have the log file generation argument. so we have to do it manually. Previously, Dr. Muniba of Bioinformatics review website was helpful in providing scripts to sort the log files.

Now the only option is the output pdbqt file. The script provided by Dr. Trott, gives errors and people have reported previously. But the issue is not resolved. The syntax error is in the line with "print" keyword as python recognises "print()" syntax.

So i changed theses line and now no error is generated but there is now output file to see any result.

Can someone help me with the matter as have a small library of 1000 compounds but without sorting them, i am stuck.

Thank you everyone in advance.

Best regards

Ayesha

Hello,

Does anyone have a syntax file for Pittsburgh sleep quality index scoring?

ECF

Hi all!

I would like to test the effectiveness of an intervention that I conducted in a randomized controlled trial design (pre-test and post-test, intervention and control group). I read that fitting linear mixed models (LMM) would do the job, and I was wondering whether anyone knows of syntax available for doing this in Mplus.

Thank you very much for helping me out.

Lara

How can I get the table tab in Amos v23?

Dear scholars!

I have collected data on the met need for EMOC (Having expected obstetric complications, treated obstetric complications, and the met need in percentage) of certain countries. Can I do a descriptive meta-analysis?

What commands in Stata can I use?

I wanted to use CMA, but it's not freely accessible.

thanks.

Melese

I have a dataset of patients with ESRD and want to estimate GFR using the 2021 CKD-EPI formula.

I would like to improve the accuracy of the frequency from the Gaussian or Orca software please which syntax will I use?

Syntax is studied in both Linguistics and Computer science, merging researches between the researchers is likely to exposes further horizons of challenges which can only be solve by the team.

Hi all,

I am looking for SPSS syntax to calculate the Framingham Risk Score of Cardiovascular disease. I need to calculate this for 500 people.

Thanks in advance for your help!

To be more specific, my experimental design is based on 3-way (4*2*2) ANOVA. Three independent variables: factor 1=type of microorganism (4 levels), factor 2=time (2 levels), and factor 3=moisture level (2 levels).

The interaction effect (microorganism*time*moisture level) was significant, but I do not know which interaction is significant.

So, in your opinion, which way is the best to use SPSS syntax in my case?

/EMMEANS=TABLES(microorganism*time*moisture_level) COMPARE(time) COMPARE(moisture_level)?

or

/EMMEANS=TABLES(microorganism*time*moisture_level) COMPARE(time)?

or

/EMMEANS=TABLES(microorganism*time*moisture_level) COMPARE(moisture_level)?

Your help is highly appreciated.

Thank you so much

Hi there,

does anyone know, how to implement more than one group in the following syntax:

calc.relimp(swiss,

type = c("lmg", "last", "first"), rela = FALSE,

groups = c("Education","Examination"), weights = abs(-23:23) )

Let´s say we have "age" and "sex" as IVs and want to run this analysis with group 1 "Education" and "Examination" and with group 2 "age" and "sex". Is there a way to do this?

Thanks in advance,

Michael

I just need to know how to specify a material in case of defining doping profile in SIlvaco.

I need to know what's going on inside a Fortran code which is not originally mine. I have a linux system and I tried the gdb debugger with some breakpoints but it didn't work( the compiler didn't compile it with -g).

I also tired using print for my variables in order to use them for plotting but after adding some lines of "print*, " syntax, the compiler again showed some errors and didn't show me any results.

I would be grateful if anyone can help me on this problem.

Respected Nick Papior,

Sir Iam using SIESTA v4.0.2

I want to fix electrode position in scattering region calculation. In manual of v4.0.2 SIESTA it is given as

%block GeometryConstraints

position from -1 to -8 # to fix atoms

%endblock GeometryConstraints

but when i tried this atoms are not fixing there respective positions.

i also tried many syntaxes to fix positions but nothing worked.

Any help will be highly appreciated.

Thanks & Regards

Shanmuk

Hello, I currently have a set of categorical variables, coded as Variable A,B,C,etc... (Yes = 1, No = 0). I would like to create a new variable called severity. To create severity, I know I'll need to create a coding scheme like so:

if Variable A = 1 and all other variables = 0, then severity = 1.

if Variable B = 1 and all other variables = 0, then severity = 2.

So on, and so forth, until I have five categories for severity.

How would you suggest I write a syntax in SPSS for something like this?

Hello, I currently have a set of categorical variables, coded as Variable A,B,C,etc... (Yes = 1, No = 0). I would like to create a new variable called severity. To create severity, I know I'll need to create a coding scheme like so:

if Variable A = 1 and all other variables = 0, then severity = 1.

if Variable B = 1 and all other variables = 0, then severity = 2.

So on, and so forth, until I have five categories for severity.

How would you suggest I write a syntax in SPSS for something like this? Thank you in advance!

I'm trying to translate the following line of Stata code into its equivalent SPSS syntax:

mixed outcome i.time c.age i.gender || id:, cov(unstr)

My understanding is that the equivalent SPSS syntax would be:

mixed outcome by time gender with age

/fixed time gender age

/random intercept | subject(id) COVTYPE(UN)

/print = solution

...and indeed, the two commands produce identical parameter estimates for the fixed effects. However, the parameter estimate for the _cons/Intercept term, standard errors and p-values they calculate are completely different. I would expect some variation in how these are calculated between programs, but this is to an unusual extent. Any thoughts?

Hello,

I want to create the tertiles in SAS to organize my NRF variable into categories. I used the below syntax to do so but the problem is that the number of observations in each category is not similar. I am wondering if there is a potential error that I missed here.

PROC UNIVARIATE DATA=master2.NRF noprint;

VAR NRF;

WEIGHT WTS_M;

OUTPUT OUT=master2.NRFTertile PCTLPTS= 33 67 PCTLPRE=NRF_P;

RUN;

DATA master2.NRF;

SET master2.NRF;

IF NRF le ..... THEN NRFTertile=1;

ELSE IF NRF gt ..... AND NRF lt ..... THEN NRFTertile=2;

ELSE IF NRF ge ..... THEN NRFTertile=3;

RUN;

Thanks,

Elsa

I think that when examining dyslexia in children, the emphasis should be on decoding, as when the child reads, it performs both alphabetic and semantic decoding of the text. ith other stages, morphosyntactic language levels

Can anyone tell me the syntax in Mathematica or MATLAB for finding the Lyapunov exponents for five-dimensional and six-dimensional systems?

Hello! My question concerns linguistics: I am looking for a method to measure recursion at the syntax level of natural languages. Are there any computerized instruments for this purpose? Which languages are they applicable to? I would appreciate any hint or publication on this issue!

I need to learn the syntax as a beginner.

Dear Professors, I have a question about my EMG data(The sampling frequency was 1500 Hz). The movement phase was different from one subject to another and had a different number of EMG data for each person. Now, how can I decrease the number of data to 100 data in each phase without changing in data Pattern for all subject's muscles (normalized to 100 data). Can I use the syntax"spline" for this goal or not? If yes, how should I use it? Please explain it. Best wishes Somayeh

We are using the SF12 in our master thesis.

We would like to know what the exact difference is between SF12 v1 and v2?

We already found a syntax for v1, but we have used the second version and could'nt find a syntax for v2.

Is it possible that anyone can send us this syntax for the second version for SPSS (/excel)?

Thanks in advance!!

Hi all,

I'm having trouble converting one particular variable in my dataset from string to numeric. I've tried manually transforming/recoding into a different variable and automatic recoding. I've also tried writing syntax (see below). The same syntax has worked for every other variable I needed to convert but this one. For all methods (manual recode, automatic recode, and writing a syntax), I end up with missing data.

recode variablename ('Occurred 0 times' = 0) ('Occurred 1 time' = 1) ('Occurred 2 times' = 2) ('Occurred 3+ times' = 3) into Nvariablename.

execute.

VALUE LABELS

Nvariablename

0 'Occurred 0 times'

1 'Occurred 1 time'

2 'Occurred 2 times'

3 'Occurred 3+ times'.

EXECUTE.

Thank you in advance for your help!

How to define *fracture criterion, type = FATIGUE in the inp file and the different material constants. If one has an example of such syntax, i would appreciate that, thank you in advance.

Hi everyone ,

I have a time series with a weekly seasonality (365 samples), and want to perform SARIMA in Eviews. Could anyone can help me to understand the estimate equation syntax for SARIMA(2,1,2)(1,1,0) with weekly seasonality?

Also should I have to use the differenced series or the actual series in the equation for the above SARIMA case.

ie, if my actual series is series 1, and the first difference is series 2 how can I write the equation for SARIMA(2,1,2)(1,1,0) with weekly seasonality

Thank you

Is there any easy to understand resource for network meta-analysis using Stata? I am looking for stata syntax for network meta-analysis.

I would like to include 90% CI for the estimate instead of the p-value, but I used Mplus to generate the standardized model results and I see that the syntax does not report confidence intervals, but "Estimate / S.E. /Est./S.E. and p -value".

I have tried several times to input ma-def2svp basis set in Gaussian Software but received a syntax error. I tried : custom=madef2svp .

ma stands for minimally augmented.

I would be very grateful if anyone kindly inform me the procedure.

What is the matlab

Hello all,

I have a dataset which contains some couples and some single people. I want to keep all the singles and keep one person from each couple. Specifically, from the couples, I want to keep the person who has the highest score between the two partners on a specific variable.

I cannot figure out how to do this with syntax. Any advice would be greatly appreciated. Thank you!

I have ecological momentary assessment (EMA) data consisting of 3 daily assessments for 14 days. The 3 daily assessments are three individual 'items', for which taking a mean is appropriate.

At the row-level I can take the mean across the items, giving me 3 time-point specific means each day for each individual. If an individual is missing an item at any specific time point I can account for that using the "mean." syntax.

I want to aggregate all three within-day timepoints up to a daily mean using 'aggregate' in SPSS, but SPSS uses all the within-day timepoints to do so, even if one is missing. Does anybody know how to overcome this issue? I've tried the MISSING = COLUMNWISE command but that omits the entire day for anyone missing anything within day.

For example: (where TP = timepoint, and '.' = missing)

TP_MEAN TP_TOTAL AGGREGATED_VAR

T1 1 2 3 2 6 3.80

T2 3 2 4 3 9 3.80

T3 . . . . . 3.80

So for the daily mean I want (1+2+3+3+2+4)/6 (= 2.5)

but using AGGREATE (MEAN TP_TOTAL), SPSS is giving me 3.80, AND filling it in at the row level for T3 where there was no timepoint data.

Does anybody know how to fix this?

Thanks!

I was trying to optimize an organoaluminium compound using the PBE0-D3(BJ)/def2-SVP level of theory. I have not used this theory before for my work. But after reading the Gaussian documentation and googling, I came up with the input like below -

But Gaussian is throwing a syntax error in the basis set input. Can anyone help me with this issue?

The gaussian output message is attached below.